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I've customized OJS for my journal (Theoretical Economics, http://econtheory.org). I'm not sure if a list of the customizations will be helpful to anyone, but here is an outline of the main changes in functionality that I have made. Possibly the list might be useful to the OJS team, who will see some of the features at least one user needs; possibly it might be useful to other users, to see what is possible.

1. Payment system added (credit cards accepted online). (An author pays a submission fee and, if their paper is accepted, may have to pay a production fee (depending on how much work they do typesetting their paper).) Users can purchase memberships, which entitle them to a free submission. Nonmembers can pay for submissions separately, if they wish. Members will be reminded about renewing their memberships.

2. Co-editors can sign up users, to use as referees. (We didn't see a way of operating without this feature---it seems that a co-editor would have to bug the Managing Editor to add a user every time they wanted to assign a referee who wasn't currently a user, which in the early days of the journal would mean almost always.)

3. Referees can upload their covering letters and reports as pdf files. In our field, and presumably in any scientific field, covering letters and reports can't be submitted as plain text, because mathematical symbols are required. The functionality for a referee to upload files exists in the default system, but it is apparently intended for a referee to upload an annotated version of their paper (an idea that we find completely bizarre, but presumably makes sense in other fields). The functionality we need requires files to have labels, indicating their type (covering letter, report, etc.).

I have made also many changes in appearance. One area where a lot of improvement can be made is in the "Submissions in Review" pages for the Managing Editor and Co-Editors: I have replaced the matrix of dates on the right hand side with text indicating the status of reports, with cases in which actions by a co-editor are required highlighted. There is one line for each active referee (ones who have declined are omitted), with text like: "John Smith: report due in 6 days" and "John Smith: report overdue 10 days" (in bold red).

I plan the following additional changes in functionality:

1. Co-editor-specific default email messages.

2. My co-editors need to be given access to the list of submitted papers and the referees to which they have been assigned, etc. I have temporarily achieved this access by enrolling all co-editors as Managing Editors, but will modify the system to allow co-editors to see the information about the papers handled by other co-editors, without being able to modify this information.

Great developments with Theoretical Economics, and thanks for sharing this as there is much to learn from here. PKP is already moving OJS in the direction of some the changes, with others for which we'd welcome the chance to incorporte TE's code and structure.
1. Payment system options for (a) author fees, (b) subscriptions and (c) pay-per-view is a natural, and we'll place this on our list for OJS 2.X
2. Co-Editors ability to enrol reviewers is underway for OJS 2.1
3. Reviewers ability to entitle uploaded files is a great idea and this appear in OJS 2.1.
4. Co-editor specific email defaults is something we'll look into implementing for OJS 2.X
5. Co-editors access to complete editorial picture is an interesting idea, although we have been concerned to protect co-editor's right to submit to the journal without compromising "blind" review, and seeing all reviewers would put that at risk. We already make it apparent in 2.0 which reviewers currently have reviews underway with the journal. So more thinking on this one for us.